Whole genome sequencing

Globally, infectious diseases account for approximately 22% of all deaths. Experts including those from the National Food Institute expect this figure will increase over the coming years due to demographic change, population density, health system inequalities, travel, trade, deforestation, and climate change. Current international disease surveillance systems are mainly based on reports made by doctors after treatment of infected patients. As a consequence, disease-causing microorganisms and resistance bacteria have time to spread unnoticed and infect large populations before finally being detected.

Until a few years ago, the hunt for the source of infection in an outbreak was considerably delayed by the fact that it could take up to several weeks for doctors and veterinarians to detect which disease-causing microorganism was the cause of the illness. One first had to grow the organism before it could be identified and subsequently typed by conventional techniques – some of which date back more than 50 years.

Meanwhile, whole genome sequencing techniques have revolutionized outbreak investigations and disease detection because they can quickly and relatively inexpensively identify a disease-causing microorganism’s entire DNA profile. By mapping bacteria's genome, it is also possible to determine their relationship and other factors such as virulence as well as antimicrobial resistance and thereby understand how bacteria are related and have evolved over time.

This new approach to disease surveillance is a paradigm shift in global disease prevention as it enables faster and more accurate identification of the source of the outbreak, thereby making it possible to reduce the spread of the disease and cost in labour and production. Whole genome sequencing can also be used to provide information on antimicrobial-resistant genes in bacteria by monitoring highly resistant clones in the population and environment.

The cost of equipment to extract bacteria’s genome sequences has fallen drastically in recent years and the sequencing process has become faster, which has helped increase the use of next generation sequencing technologies.

Global data sharing

The National Food Institute carries out research using whole genome sequencing techniques. As such, the institute is helping to set the international standard for the detection, surveillance and studies of the global spread of disease-causing microorganism and antimicrobial-resistant bacteria. The institute is also working to advance and build next generation sequencing capacity internationally.

As such, researchers from the National Food Institute and DTU Systems Biology head up a large EU project called COMPARE with 28 European partners. In the research project, the partners want to develop a global platform that will enable real time exchange and interpretation of information about disease-causing microorganisms from around the world and to compare this with other relevant information such as clinical and epidemiological data.

The platform will be used to harmonize the way scientists, authorities, doctors and organizations around the world collect samples, generate genome sequencing data and carry out risk assessments. This new approach to disease surveillance will be able to revolutionize the way we combat diseases globally. The aim is that the data which is generated can be used to quickly implement targeted initiatives that can save lives and prevent the diseases from spreading – both locally and globally. 

Read more about the five-year research project in the National Food Institute’s press release from 20 January 2015: Large EU project to head up global fight against infectious diseases and on COMPARE's website.

The National Food Institute is also one of the driving forces behind an initiative called Global Microbial Identifier, GMI. The GMI initiative is aimed at building an open-source internet-based solution that collects and shares data on species, type and antimicrobial resistance based on genome sequence data. The GMI initiative has particular potential in developing countries where the new technology can be applied directly as a part of establishing better health and food safety systems.

In GMI, the National Food Institute is involved in several of the working groups focusing on political issues that hamper the expansion of the technology in developing countries, creating the necessary IT infrastructure, developing online tools and the first worldwide proficiency tests on genomics. 

Read more about GMI on the website: Global Microbial Identifier.

New knowledge about old outbreaks

Whole genome sequencing can help us better understand the past so this knowledge can be used to better tackle today’s problems with infectious diseases and antimicrobial resistance. Using genome sequencing techniques, researchers from the National Food Institute have e.g. analyzed 315 samples of Salmonella Typhimurium DT 104 from both humans and animals.

The samples had been collected from 1969 to 2012 in 21 different countries on six continents. Using the new data the institute’s scientists have both uncovered the bacteria’s origin and established when it became resistant to common antimicrobials.

Read more in the National Food Institute’s news item from 29 March 2016: Knowledge of bacteria’s origin and spread can prevent disease.

Using waste water to prevent disease

Sewage systems are an important source of disease-causing microorganisms particularly in densely populated areas with poor infrastructure.

In a project at the National Food Institute, researchers are investigating whether it is possible to quickly and relatively cheaply generate large quantities of data from around the world, which can accurately show what disease-causing microorganisms are prevalent in a particular area as well as how many bacteria are resistant to antimicrobial treatment.

In the project two litres of sewage waste water collected from more than 70 locations around the world will be analyzed using whole genome sequencing. The generated data can be used to identify and prevent infectious diseases and give important information in the fight against resistant bacteria, viruses and parasites.